#[RUN: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Script/pipe_UMI_IDT_MS_SimulRefVersion_etap1_byLane.sh /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/Data/Intensities/BaseCalls/ /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/SampleSheetUsed.csv 2 220204_NS500487_0027_AHFCJLAFX3 /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output/ Y ]
# ========= [INFO] ==========
# inputBCLdir    : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/Data/Intensities/BaseCalls/
# sampleSheetFile: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/SampleSheetUsed.csv
# barcodesFileIn : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.barcodeFile.txt
# Dossier Output : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output/
# barcodesMetrics: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.barcode_metrics.txt
# BC Out : /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//1_Barcodes_L2/
# BAM Out: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//2_BAM_L2/
# Len_R1 : 142
# Len_R2 : 151
# Run BC : 220204_NS500487_0027_AHFCJLAFX3
# LIBRARY: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.LIBRARY_PARAMS.txt
# LogFile: /env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.UMI_IDT.log
# Lane No: 2
# 2Barcod: Y
# R_Struc: 142T8B9M8B151T
# =============================
#
module load picard/2.8.2
====== [ Demultiplex with UMI ] ====== 
>java -jar /env/gfs/apps/picard/2.8.2/picard.jar ExtractIlluminaBarcodes BASECALLS_DIR=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/Data/Intensities/BaseCalls/ BARCODE_FILE=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.barcodeFile.txt READ_STRUCTURE=142T8B9M8B151T LANE=2 OUTPUT_DIR=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//1_Barcodes_L2/ METRICS_FILE=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.barcode_metrics.txt
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar IlluminaBasecallsToSam BASECALLS_DIR=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Input/220204_NS500487_0027_AHFCJLAFX3/Data/Intensities/BaseCalls/ BARCODES_DIR=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//1_Barcodes_L2/ LANE=2 READ_STRUCTURE=142T8B9M8B151T RUN_BARCODE=220204_NS500487_0027_AHFCJLAFX3 LIBRARY_PARAMS=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//220204_NS500487_0027_AHFCJLAFX3_L2.LIBRARY_PARAMS.txt TMP_DIR=/env/gnfs/Projects/DETECT_SENSI_MSI/Papier//Example/Example_II.1/Output//java_io_tmpDir_L2/ MOLECULAR_INDEX_TAG=RX ADAPTERS_TO_CHECK=INDEXED
========[ END ]========
